AlignACE version 2.2 July 7, 1998 alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jtyrR.reg -g0.5 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.5 maxlen = 30 weight = 0.8 exclude = 158 Input sequences: #1 aroP 300 bp aroP 457 1-1374 CDS #2 aroL 182 bp aroL 174 1-525 CDS #3 aroG 300 bp aroG 350 1-1053 CDS #4 tyrR 147 bp tyrR 513 1-1542 CDS #5 tyrP 190 bp tyrP 403 1-1212 CDS #6 aroF 170 bp aroF 356 1-1071 CDS #7 mtr 153 bp mtr 414 1-1245 CDS #8 tyrB 192 bp tyrB 397 1-1194 CDS Motif number 1 TTGAGAGGGGTTGAGGCTGAGCTTTACAAACGGTTTCT 1 77 1 TTGATTTACA 0.89517 -224 TTCCGTTTGTTGTATTAATTTGTTTACATCAAAGAAGT 1 213 0 TGTATTTACA 0.910375 -88 ATACAACAAACGGAATTGCAAACTTACACACGCATCAC 1 236 1 CGGACTTACA 0.873881 -65 ATGTAATTTATTATTTACACTTCATTCTT 2 2 1 TGTATTTACA 0.553412 -181 TAGTAAGGGGTGTATTGAGATTTTCACTTTAAGTGGAA 2 55 1 TGTATTCACT 0.847899 -128 TCACTTTAAGTGGAATTTTTTCTTTACAATCGAAATTG 2 78 1 TGGATTTACA 0.909043 -105 CCGTTCATAGTGTAAAACCCCGTTTACACATTCTGACG 3 213 1 TGTATTTACA 0.499977 -88 TGCTTTTTATTGTACATTTATATTTACACCATATGTAA 5 82 1 TGTATTTACA 0.557701 -109 CCCTTACCTCTGTATAGATAAATTTACACTCCCT 6 7 0 TGTATTTACA 0.557701 -164 ATCCATATTTCGTACATTTTTATTTACACAGGCAATTT 6 59 0 CGTATTTACA 0.892376 -112 GTACGAAATATGGATTGAAAACTTTACTTTATGTGTTA 6 82 1 TGGATTTACT 0.963862 -89 AAATCGGGGCTGTATATATTATTTTACAGATTGTGTTC 7 26 0 TGTATTTACA 0.557701 -128 **** ****** Masking position 4 Map Score: 23.2628 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 5 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 TAATGGTATGCGGCAGCGAATGCACCCGCT 1 146 0 CGGCAGCGAA 0.901968 -155 AATTTGTTTACATCAAAGAAGTTTGAATTG 1 205 0 CATCAAAGAA 0.850767 -96 AATAAATATTCAAGAATGAAGTGTAAATAA 2 21 0 CAAGAATGAA 0.73184 -162 TTATGAAACGCAGCAGAGAATCTTGAAATA 3 90 1 CAGCAGAGAA 0.980945 -211 TGCGCCAGCGCAGGACTGAATGCTTTTTAT 5 62 1 CAGGACTGAA 0.957829 -129 TAAAGATCGTCAGGACAGAAGAAAGC 5 175 1 CAGGACAGAA 0.981207 -16 CTATTTTTCACTGGAGAGAAGCCCTC 7 138 1 CTGGAGAGAA 0.947093 -16 TTTATAAGAGCATGAAAGAACATCAACTTA 8 29 0 CATGAAAGAA 0.917097 -164 AGTGGATGTTCAGGAGCGAACGGCAATTAG 8 107 0 CAGGAGCGAA 0.985341 -86 ********** Masking position 5 Map Score: 7.56665 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 300 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 CGCTTTATGCATGGTTGAAGATGAGTTGCT 1 120 0 ATGGTTGAAG 0.724101 -181 TATTCTTGATCTGACGGAAGTCTTTTTGTA 1 174 1 CTGACGGAAG 0.986463 -127 TGGTCGTTATGTCGGATAACCTCTTCCA 3 9 1 ATGTCGGATA 0.708094 -292 TGCAAATGCACTGTTGGAAGAGGTTATCCG 3 23 0 CTGTTGGAAG 0.944288 -278 GTTTCATAACCTGGCTGAAATCTTAAACCA 3 69 0 CTGGCTGAAA 0.951478 -232 TTTACACATTCTGACGGAAGATATAGATTG 3 235 1 CTGACGGAAG 0.986463 -66 CAGTCCTGCGCTGGCGCAAAGTCTTCATAA 5 50 0 CTGGCGCAAA 0.933268 -141 GGTCGTGCCTCTGGCGGATGTACGTTTGTC 8 59 1 CTGGCGGATG 0.987647 -134 ********** Masking position 8 Map Score: 6.18092 Number of sites scoring better than the average of aligned sites = 2157 Number in coding regions = 2090 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 4 CGAATGCACCCGCTTTATGCATGGTTGAAG 1 130 0 CGCTTTATGC 0.814369 -171 TCTGACGGAAGTCTTTTTGTAACAATTCAA 1 183 1 GTCTTTTTGT 0.925159 -118 TCGTGCGGTGGTTGTTTTTTTGATCTACGC 1 275 0 GTTGTTTTTT 0.703326 -26 TGGTCGTTATGTCGGATAACCT 3 3 1 GTCGTTATGT 0.941527 -298 TAGGAGAGATCTCGTTTTTCGCGACAATCT 3 153 1 CTCGTTTTTC 0.904577 -148 GCGACAATCTGGCGTTTTTCTTGCTAATTC 3 173 1 GGCGTTTTTC 0.967307 -128 CGCCGAAGTGCCCGTTTTTCCGTCTTTGTG 4 42 1 CCCGTTTTTC 0.842965 -106 CCGTTTTTCCGTCTTTGTGTCAATGATTGT 4 53 1 GTCTTTGTGT 0.766536 -95 CGCTACGCTAGGCTTTTTTTGAGGAGGGAC 5 12 0 GGCTTTTTTT 0.893248 -179 TGACGAAGCAGCCGTTATGCCTTAACCTGC 5 128 1 GCCGTTATGC 0.935872 -63 TTACCATCGGGGCTTTTTTTCTGTCTTTTG 7 64 1 GGCTTTTTTT 0.893248 -90 GTGCGACTGCGTTGTTATGCATTGCACTGT 7 109 0 GTTGTTATGC 0.781696 -45 ********** Masking position 5 Map Score: 5.91666 Number of sites scoring better than the average of aligned sites = 2299 Number in coding regions = 2049 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 5 TGTTGTATTAATTTGTTTACATCAAAGAAGT 1 213 0 ATTTTTTACA 0.955432 -88 ATGTAATTTATTATTTACACTTCATTCTT 2 9 1 TATTTTTACA 0.806327 -174 AAGTGGAATTTTTTCTTTACAATCGAAATTG 2 85 1 TTTTTTTACA 0.963517 -98 TGCTGACCGGATATCTTTACGCCGAAGTGCC 4 23 1 ATATTTTACG 0.724324 -125 CTGAATGCTTTTTATTGTACATTTATATTTA 5 77 1 TTTATGTACA 0.763977 -114 TATTGTACATTTATATTTACACCATATGTAA 5 89 1 TTATTTTACA 0.932681 -102 CTCTGTATAGATAAATTTACACTCCCT 6 7 0 ATAATTTACA 0.855051 -164 TTTCGTACATTTTTATTTACACAGGCAATTT 6 59 0 TTTTTTTACA 0.963508 -112 GGCTGTATATATTATTTTACAGATTGTGTTC 7 26 0 ATTATTTACA 0.918337 -128 **** ****** Masking position 6 Map Score: 6.03909 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 27 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 ACAATCGAAATTGTACTAGTTTGATGGTATGATCGC 2 103 1 TTTCGTTTTG 0.985084 -80 GAAGTGCCCGTTTTTCCGTCTTTGTGTCAATGATTG 4 46 1 TTTCTCTTTG 0.872716 -102 ATCATATTAATTGTTCTTTTTTCAGGTGAAGGTTCC 4 121 1 TTTCTTTTGG 0.97616 -27 GCGATCCTGTTTATGCTCGTTTGCGATAGTTGATCC 6 141 0 TTTCGTTTGA 0.921244 -30 TTTCTGTCTTTTGTACTCGTGTACTGGTACAGTGCA 7 81 1 TTTCGTGTTG 0.946057 -73 GAACATCAACTTATTGAATTTTTAGGATTTT 8 6 0 TTTGTTTTGG 0.871413 -187 GATCTTCGCCTTCTTCCGGTTTATTGTGTTTTAACC 8 138 1 TTTCGTTTTG 0.985084 -55 GCGATGGTTCTCCAGGTTTACGGGCAGGTGGTT 8 170 0 TTTCGTTTGG 0.990544 -23 ** * * **** ** Masking position 12 Map Score: 3.70502 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 122 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 CAATGCCTTATATTCACCTGCAAATGCACT 3 41 0 TATTCACCTG 0.965111 -260 CTGCTGCGTTTCATAACCTGGCTGAAATCT 3 76 0 TCATAACCTG 0.950751 -225 GGGAACCTTCACCTGAAAAAAGAAC 4 133 0 CCTTCACCTG 0.985355 -15 AGCCGTTATGCCTTAACCTGCGCCGCAGAT 5 137 1 CCTTAACCTG 0.967597 -54 TATTGTGTTTTAACCACCTGCCCGTAAACC 8 159 1 TAACCACCTG 0.89687 -34 ********** Masking position 6 Map Score: 0.936689 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 227 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 ATCAAAAAAACAACCACCGCACGAGGTTTC 1 281 1 CAACCACCGC 0.929193 -20 CTCATGACACCGGCTTTCGCCGCATTGCGA 2 143 1 CGGCTTTCGC 0.972726 -40 GGAGAGATCTCGTTTTTCGCGACAATCTGG 3 155 1 CGTTTTTCGC 0.781039 -146 TCTTCATAAGCGGCAATCGCTACGCTAGGC 5 29 0 CGGCAATCGC 0.9484 -162 CGCTGAGGATCAACTATCGCAAACGAGCAT 6 135 1 CAACTATCGC 0.964441 -36 AACATCCACTCGATCTTCGCCTTCTTCCGG 8 127 1 CGATCTTCGC 0.948596 -66 TAAACCTGGAGAACCATCGC 8 183 1 GAACCATCGC 0.891292 -10 ********** Masking position 8 Map Score: 0.945407 Number of sites scoring better than the average of aligned sites = 1369 Number in coding regions = 1329 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 9 TCAACCCCTCTCAATATGTAGAATGAATTTA 1 60 0 TCAATTGTAG 0.790402 -241 TTAAAAAGAAACCGTTTGTAAAGCTCAGCCT 1 90 0 ACCGTTGTAA 0.960491 -211 TACGCAGTGATGCGTGTGTAAGTTTGCAATT 1 249 0 TGCGTTGTAA 0.903047 -52 GATCTCTCCTACAATTTCTAACTGTAACTCC 3 133 0 ACAATTCTAA 0.790344 -168 ATCTTCCGTCAGAATGTGTAAACGGGGTTTT 3 226 0 AGAATTGTAA 0.933331 -75 TTATATTTACACCATATGTAACGTCGGTTTG 5 99 1 ACCATTGTAA 0.973066 -92 GCGACTAAATTGCCTGTGTAAATAAAAATGT 6 53 1 TGCCTTGTAA 0.835015 -118 AACAGCGAACACAATCTGTAAAATAATATAT 7 20 1 ACAATTGTAA 0.957942 -134 ***** ***** Masking position 10 Map Score: 1.03049 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 66 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 10 TTGTAAAGCTCAGCCTCAACCCCTCTCAAT 1 76 0 CAGCCTCAAC 0.938049 -225 CATCCTCGCTGAGGATCAACTATCGCAAAC 6 129 1 GAGGATCAAC 0.968142 -42 TATCGCAAACGAGCATAAACAGGATCGCCA 6 149 1 GAGCATAAAC 0.957747 -22 GAGCATGAAAGAACATCAACTTATTGAATT 8 22 0 GAACATCAAC 0.981296 -171 GTTCGCTCCTGAACATCCACTCGATCTTCG 8 116 1 GAACATCCAC 0.959094 -77 ********** Masking position 6 Map Score: 0.221856 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 394 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 ********** No masking Map Score: -3.1879e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 12 ********** No masking Map Score: -3.1879e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: -3.1879e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0